title: Multiplex bisulfite sequencing identifies differentially methylated regions in target genes in embryonic cardiomyocytes following knockdown of DNMT1 expression

status: Public on May 12 2019

city: Gainesville

first: Xiefan

last: Fang

state: Florida

address: 1200 Newell Drive, ARB R1-148

department: Pediatrics

institute: University of Florida

summary: Purpose: This study aims to identify the differentially methylated regions in target genes in embryonic cardiomyocytes following the knockdown of DNMT1 expression. Methods: Primary cardiomyocytes were isolated from mouse embryonic day (E) 13.5 ventricles, and cultured for 48 h at 37°C to reach 70-80% confluency. Cells were transfected with either Qiagen FlexiTube GeneSolution (with 4 siRNAs) DNMT1 siRNA (#GS13433) or AllStars negative control siRNA (#1027281) at 12 nM using lipofectamine RNAiMAX (n=3 per treatment). At 72 h after transfection, cells were released with Accutase (Innovative Cell Technologies, San Diego, CA) and dissociated with Accumax (Innovative Cell Technologies). To sort cardiomyocytes, dissociated cells were stained with anti-VCAM1 antibody conjugated with allophycocyanin (APC; BioLegend, San Diego, CA), followed by magnetic sorting using anti-APC microbeads and magnetic assisted cell sorting (MACS) columns (Miltenyi Biotec, Bergisch Gladbach, Germany). DNA was extracted with the Quick-gDNA™ MicroPrep kit (Zymo Research, Irvine, CA). Genomic DNA was treated with sodium metabisulfite for bisulfite conversion. Target gene regions for fifteen target genes (two promoter regions per gene) were PCR-amplified from the bisulfite-converted DNA with ZymoTaq™ PreMix (Hot start DNA taq polymerase, ZYMO Research, Irvine, CA). The fifteen genes include Myh6, Myh7, Myh7b, Nppa, Nppb, Tnnc1, Tnni3, Tnnt2, Camta1, Camta2, Cdkn1A, Cdkn1B, Cdkn1C, Mef2c, and Mef2d. PCR products were cleaned with the ZR-96 DNA Clean & Concentrator™-5 kit (ZYMO Research). PCR products from the same genomic DNA sample were pooled at equal concentration ratio and made into an indexed sequencing library with the Nextera XT DNA Library Preparation kit and the Nextera XT Index Kit (Illumina, San Diego, CA). The Illumina-adapted libraries were pooled at equal molar ratio, spiked with 20% PhiX control libraries (Illumina), and sequenced with one 1x150 cycles run (v3) on a MiSeq sequencer (Illumina). The fastq files generated from MiSeq were uploaded to the UF Research Computing Galaxy instance developed by the University of Florida. The data were cleaned with the following steps: removed sequencing artifacts, trimmed 5’ or 3’ ends with low scores, removed adaptor contamination, and filtered low quality reads by the FastQC program. A reference genome with the amplicon sequences was built and bisulfite converted in silico with Bismark Bisulfite Mapper. The high quality sequence reads were aligned to the reference genome using Bowtie 2. Cytosine methylation counting was performed with the Bismark methylation extractor. Differential methylation was analyzed with the Methylkit package. CpG sites with false discovery rate (FDR) less than 0.05 and absolute percent methylation difference greater than 5% were considered as significant. Results: Following knockdown of DNMT1 for 72 h, differentially methylated regions were identified in the promoter CpG sites of Myh6, Myh7, Myh7b, Tnnc1, Tnni3, Tnnt2, Nppa, Nppb, Mef2c, Mef2d, Camta2, Cdkn1A, and Cdkn1C.

overall_design: The DNA methylation patterns of target promoters in embryonic cardiomyocytes with knockdown of DNMT1 expression were generated by deep sequencing (n=3 for negative siRNA and n=3 for DNMT1 siRNA), using Illumina MiSeq.

first: Scott

middle: A

last: Rivkees

first: Christopher

last: Wendler


title: RNA sequencing identifies differentially expressed genes in embryonic cardiomyocytes following knockdown of DNMT1 expression for 72 h

status: Public on May 13 2019

country: USA

type: Expression profiling by high throughput sequencing

summary: Purpose: This study aims to identify the differentially expressed genes in embryonic cardiomyocytes following the knockdown of DNMT1 expression. Methods: Primary cardiomyocytes were isolated from mouse embryonic day (E) 13.5 ventricles, and cultured for 48 h at 37°C to reach 70-80% confluency. Cells were transfected with either Qiagen FlexiTube GeneSolution (with 4 siRNAs) DNMT1 siRNA (#GS13433) or AllStars negative control siRNA (#1027281) at 12 nM using lipofectamine RNAiMAX (n=3 per treatment). At 72 h after transfection, cells were released with Accutase (Innovative Cell Technologies, San Diego, CA) and dissociated with Accumax (Innovative Cell Technologies). To sort cardiomyocytes, dissociated cells were stained with anti-VCAM1 antibody conjugated with allophycocyanin (APC; BioLegend, San Diego, CA) and magnetically sorted using anti-APC microbeads and magnetic assisted cell sorting (MACS) columns (Miltenyi Biotec, Bergisch Gladbach, Germany). Total RNA was isolated from the sorted cardiomyocytes with the RNAqueous®-Micro Total RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA). RNA-Seq libraries were prepared with the NEBNext® mRNA Library Prep Master Mix Set for Illumina and NEBNext Multiplex Oligos for Illumina (NEB, Ipswich, MA). The Illumina-adapted libraries were pooled at equal molar ratio and sequenced with one High Output 1x75 cycles run on a NextSeq500 sequencer (Illumina). The fastq files generated from RNA-Seq were uploaded to the UF Research Computing Galaxy instance developed by the University of Florida. The data were cleaned with the following steps: removed sequencing artifacts, trimmed 5’ or 3’ ends with low scores, removed adaptor contamination, and filtered low quality reads by the FastQC program. The remaining high quality RNA-Seq reads were mapped to the mouse genome (mm10) with the Tophat2 tool. Counting of RNA-seq reads were performed with HTSeq. Differential expression (DE) of genes between treatments was analyzed using two methods: R packages EdgeR and DEseq2, with Ensembl Mus_GRCm38.79.gtf as the reference annotation. Genes with false discovery rate (FDR) less than 0.05 and absolute fold change greater than 1.5 were considered as significant. Unique DE genes were identified by combining the results generated from the two analytical methods. Results: DE analysis by DEseq2 and EdgeR software revealed that 801 genes were up-regulated, and 494 genes were down-regulated after knockdown of DNMT1 expression for 72 h.

overall_design: The mRNA profile in embryonic cardiomyocytes with knockdown of DNMT1 expression was generated by deep sequencing (n=3 for negative siRNA and n=3 for DNMT1 siRNA), using Illumina NextSeq500.

middle: C


title: Genome-wide map of open-chromatin region in Leukemia cell-lines

status: Public on Mar 31 2019

city: La Jolla

first: Arko

last: Sen

state: California

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed ATAC-seq on publicly available leukemia cell-lines and used them to predict  non-coding regulatory mutations in open-chromatin regions of the genome.

overall_design: Examination of open chromatin regions in the leukemia cell-lines

first: Graham

last: McVicker


title: Knockdown of the Prolactin Receptor Inhibits Recruitment of Tregs and their Promotion of EMT in a Syngeneic Breast Cancer Model

status: Public on Feb 28 2019

city: Cleveland

first: Kuan-Hui

middle: Ethan

last: Chen

state: MS

address: 1003 W Sunflower Rd

institute: Delta State University

summary: The clinical relevance and prognostic significance of tumor-infiltrating Tregs in different types of cancers makes them appealing therapeutic targets. However, while effective at inhibiting cancer progression, immunotherapeutics targeting Treg function have adverse effects in a substantial proportion of patients, ranging from mild inflammatory disorders to frank autoimmune disease. Here, we report that systemic knockdown of the long form of the prolactin receptor (LFPRLR) inhibits recruitment of Tregs to primary tumors and, importantly, metastasis-promoting activities of tumor Tregs, with no change in the production of TGFβ or IL-10 by tumor Tregs or the ability of peripheral Tregs to suppress anti-CD3/CD28-stimulated effector cell proliferation. Knockdown of the LFPRLR was accomplished using a derivatized DNA splice-modulating oligomer and outcome was assessed in the highly-metastatic, syngeneic, orthotopic 4T1-Balb/c immune-competent breast cancer model. We conclude that knockdown of the LFPRLR produces a more functionally-specific anti-cancer effect in Tregs, suggesting promise as a future therapeutic approach.

overall_design: mice were orthotopically injected with 4T1 breast cancer cells treated with other control splice modulating oligomer or LFPRLR splice modulating oligomer for 12 days. Whole tumor or sorted tumor Tregs were collected and the gene expression was analyzed by RNAseq between the control and LFPRLR treated mice. N=6 in each group.

middle: E

first: Mrinal

last: Ghosh

first: Lorena

last: Rivera

first: Mary

middle: Y

last: Lorenson

first: Ameae

middle: M

last: Walker


title: Transcriptomic profile of zebrafish cardiomyocytes throughout heart development

status: Public on Jan 10 2019

city: Warsaw

first: Michal

last: Pawlak

address: Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology

summary: By using transgenic zebrafish lines Tg(nxk2.5:GFP) (Witzel et al. 2012) and Tg(myl7:EGFP) (D'Amico et al. 2007), we have characterized transcriptomic profile of FACS-isolated CM (GFP+) from developing zebrafish heart at 24, 48 and 72 hpf, corresponding to heart tube formation, chamber formation and differentiation and heart maturation, respectively. GFP- cells were used as a control. We have identified cardiac regulatory networks playing a crucial role in heart morphogenesis. To validate their importance in heart development, we employed zebrafish mutants of cardiac transciption factors Gata5, Hand2 and Tbx5a, the disruption of which were previously linked to impaired migration of the cardiac primordia to the embryonic midline, reduced number  of  myocardial  precursors and failure of heart looping, respectively (Reiter et al. 1999; Yelon et al. 2000; Garrity et al. 2002). RNA-seq was performed from homozygous gata5tm236a/tm236a, tbx5am21/ m21, hand2s6/s6 mutant 72 hpf embryos in Tg(myl7:EGFP) genetic background. Homozygous mutant embryos for analyses were selected on the basis of their phenotypes of cardia bifida (gata5tm236a/tm236a, hand2s6/s6) or heart-string (tbx5am21/ m21) .

overall_design: Examination of transcriptomic profile of cardiomycytes at 3 stages of heart development

first: Cecilia

middle: L

last: Winata


title: Conditional Activation of NF-kB Inducing Kinase (NIK) in the Osteolineage Enhances both Basal and Loading-Induced Bone Formation

status: Public on Jun 25 2019

city: Saint Louis

first: Bo

last: Zhang

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

summary: Studies from global loss-of-function mutants suggest that alternative NF-kB downstream of NF-kB inducing kinase (NIK) is a cell-intrinsic negative regulator of osteogenesis.  However, the interpretation of the osteoblast and/or osteocyte contribution to the bone phenotype is complicated by simultaneous osteoclast defects in these models.  Therefore, we turned to a transgenic mouse model to investigate the direct role of NIK in the osteolineage.  Osx-Cre;NT3 animals (NT3-Cre+), which bear a constitutively active NIK allele (NT3) driven by Osx-Cre, were compared to their Cre-negative, Control (Ctrl)  littermates.  NT3-Cre+ mice had elevated serum P1NP and CTX  levels.  Despite this high turnover state, microCT showed that constitutive activation of NIK resulted in a net increase in basal bone mass in both cortical and cancellous compartments.  Furthermore, NT3-Cre+ mice exhibited a greater anabolic response following mechanical loading compared to controls.  We next performed RNA-Seq on non-loaded and loaded tibiae to elucidate possible mechanisms underlying the increased bone anabolism seen in NT3-Cre+ mice.  Hierarchical clustering revealed two main transcriptional programs: one loading-responsive and the other NT3 transgene-driven.  Gene ontology (GO) analysis indicated a distinct upregulation of receptor, kinase and growth factor activities including Wnts, as well as a calcium-response signature in NT3-Cre+ limbs.  The promoters of these GO-term associated genes, including many known to be bone-anabolic, were highly enriched for multiple kB recognition elements (kB-RE) relative to the background frequency in the genome.  The loading response in NT3-Cre+ mice substantially overlapped (>90%) with Ctrl.  Surprisingly, control animals had 10-fold more differentially expressed genes (DEGs) in response to loading.  However, most top DEGs shared between genotypes had a high incidence of multiple kB-RE in their promoters.  Therefore, both transcriptional programs (loading-responsive and NT3 transgene-driven) are modulated by NF-kB.  Our studies uncover a previously unrecognized role for NF-kB in the promotion of both basal and mechanically-stimulated bone formation.

overall_design: Differential gene expression in Ctrl vs NT3-Cre+ non-loaded and loaded limbs.  16 total samples.  n=4 each genotype (Ctrl or NT3-Cre+) as biological replicates.  Paired non-loaded and loaded samples for each mouse.

first: Jennifer

last: Davis

first: Linda

last: Cox

first: Christine

last: Shao

first: Cheng

last: Lyu

first: Shaopeng

last: Liu

first: Rajeev

last: Aurora

first: Deborah

middle: J

last: Veis


title: Transcriptome profile and Genome-wide chromatin accessibility profile of zebrafish cardiomyocytes throughout heart development

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Deciphering the genomic, epigenomic and transcriptomic landscapes of pre-invasive lung cancer lesions to determine prognosis II

status: Public on Jan 01 2019

city: London

first: Vitor

middle: H

last: Teixeira

address: 5 University Street

department: Medicine

country: United Kingdom

institute: University College London

summary: Background: Lung carcinoma-in-situ (CIS) lesions are the pre-invasive precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Whether modern molecular profiling techniques can identify those pre-invasive lesions that will subsequently progress and distinguish them from those that will regress is unknown.   Methods: Progressive and regressive CIS lesions were laser-captured and their genome, epigenome and transcriptome interrogated. We analysed 83 progressive lesions, 41 regressive and 33 normal epithelial control samples. DNA methylation and gene expression profiles were further validated using publicly available lung cancer data.   Results: Somatic mutation burden was higher in progressive lesions than regressive CIS lesions, across base substitutions, rearrangements, insertions and deletions. Driver mutations were present in both progressive and regressive CIS lesions, but were more numerous in progressive cases. Progressive and regressive CIS lesions had distinct epigenomic and transcriptional profiles, with a strong chromosomal instability signature. Gene expression, methylation and copy number profiles can all predict accurately which CIS lesions will progress to lung cancer.  Conclusion: Pre-invasive CIS lesions that will subsequently progress to invasive lung cancer can be distinguished from those that will regress using molecular profiling. Progression is associated with a strong chromosomal instability signature. These findings inform the development of novel therapeutic targets.

overall_design: Progressive and regressive lung CIS lesions were laser-captured and their transcriptome interrogated. This data set represents a validation cohort. CIS gene expression profiles were further validated using publicly available lung cancer data.

first: Adam

last: Pennycuick


title: Deciphering the genomic, epigenomic and transcriptomic landscapes of pre-invasive lung cancer lesions to determine prognosis

type: Methylation profiling by genome tiling array


title: Deciphering the genomic, epigenomic and transcriptomic landscapes of pre-invasive lung cancer lesions to determine prognosis I

summary: Rationale: Lung carcinoma-in-situ (CIS) lesions are the pre-malignant precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Whether modern molecular profiling techniques can identify those preinvasive lesions that will subsequently progress and distinguish them from those that will regress is unknown. We performed gene expression microarrays on CIS lesions, with a view to deriving a molecular signature predictive of future progression to invasive cancer.

overall_design:
Progressive and regressive lung CIS lesions were laser-captured and their transcriptome interrogated. We analysed 17 progressive and 16 regressive CIS lesions. CIS gene expression profiles were further validated using publicly available lung cancer data.

Please note that the probe-level raw data is unavailable. Thus, only the gene-level raw data was included in the records.


title: Plasma lncRNA and mRNA profiles in patients with NSCLC: Pre-operation vs. post-operation

status: Public on Dec 31 2018

city: Shenzhen

first: Rihong

last: Zhai

state: Guangdong

address: 1066 Xueyuan Ave.

country: China

institute: Shenzhen University School of Medicine

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Circulating transcriptional landscapes between pre-operation and post-operation plasma samples were compared using the Arraystar Human LncRNA Microarray V4 with probes for profiling of 40173 human lncRNAs and 20730mRNAs. Goal was to investigate the impact of tumor removal on circulating lncRNA and mRNA expression levels.

overall_design: Pre-operation vs. post-operation


title: Gene expression profiling of Hodgkin Lymphoma and Non-Hodgkin Lymphoma cell lines for the NF-kB family of trasncription factors followinf each one depletion by shRNA.

city: CABA

first: Stella

last: Ranuncolo

state: Buenos Aires

address: Potosí 4240

country: Argentina

institute: Instituto Universitario del Hospital Italiano (IUHI)

summary: NF-kB transcription factors regulate different sets of genes in distinct germinal center derived B-cell lymphomas

overall_design: Total ARN from U-H01 and HBL-1 cell lines was prepared from wild tyoe cells and after knocking down the expression of Rel-A, Rel-B and cRel in both of them.

last: Ranuncolo.


title: Deciphering the genomic, epigenomic and transcriptomic landscapes of pre-invasive lung cancer lesions to determine prognosis III

overall_design: Progressive and regressive lung CIS lesions were laser-captured and their epigenome interrogated. Results were further validated using publicly available lung cancer data.

first: Christodoulos

middle: P

last: Pipinikas


title: Pheripheral blood cells expression data from 18 hemochromatosis patients, with various mutations for hemochromatosis, and 6 gender and aged matched healty controls.

status: Public on Dec 23 2018

city: Grålum

first: camilla

middle: furlund

last: nystrand

address: Kalnesveien 320

country: Norway

institute: Østfold hospital trust

summary: Using PAXgene tubes, pheripheral blood samples were colleted from 18 hemochromatosis patients. The patients were dividen into two groups; 12 patients that were C282Y homozygotes (group 1) and 6 patients who were H63D homozygotes or H63D/C282Y heterozygotes (group 2). Expression profiles were compared with 6 gender and aged matched healthy controls (group 3).

overall_design:
18 patients samples and 6 control samples were performed.

***Please note that all sample records have been updated on Feb 26, 2020 as per submitter's request.

first: Heidi

middle: K

last: Grønlien

first: Trine

last: Christoffersen

first: Camilla

middle: F

last: Nystrand

first: Lamya

last: Garabet

first: Terje

last: Syvertsen

first: Morten

last: Moe

first: Ole

last: Olstad

last: Jonassen


title: Stoichiometric Production of Protein-Complex Components in Eukaryotes Without Widespread Feedback Regulation

status: Public on Dec 03 2018

city: Boston

first: James

middle: Christopher

last: Taggart

state: MA

address: 200 Longwood Avenue

department: Systems Biology

institute: Harvard Medical School

summary: Constituents of multi-protein complexes are required at well-defined levels relative to each other. However, it remains unknown whether eukaryotic cells typically produce precise amounts of subunits, or instead rely on degradation to mitigate imprecise production. Here we quantified the production rates of multi-protein complexes in single- and multi-cellular eukaryotes using ribosome profiling. By resolving read-mapping ambiguities present in a large fraction of ribosome footprints which often distorts quantitation accuracy in eukaryotes, we found that obligate components of multi-protein complexes are produced in proportion to their stoichiometry, indicating that their abundances are already precisely tuned at the synthesis level. By systematically interrogating the impact of gene dosage variations in budding yeast, we found a general lack of negative feedback regulation protecting the normally precise rates of subunit synthesis. These results reveal a core principle of proteome homeostasis and highlight the evolution towards quantitative control at every stage of the central dogma.

overall_design: 13 ribosome profiling experiments in Saccharomyces cerevisiae

first: Gene-Wei

last: Li


title: circ-ZNF609 regulates G1-S progression in Rhabdomyosarcoma

status: Public on Dec 14 2018

city: Rome

first: Francesca

last: Rossi

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

summary: Circular RNAs (circRNAs) represent a class of covalently closed RNAs, derived from a non-canonical splicing event, ubiquitously expressed among Eukaryotes and conserved among different species. We identified a circRNA (circ-ZNF609) involved in the regulation of human primary myoblast proliferation. Upon its depletion, the percentage of proliferating myoblasts was highly reduced. To deepen our knowledge about circ-ZNF609 role in cell cycle regulation, we studied its expression and function in Rhabdomyosarcoma (RMS), a pediatric skeletal muscle malignancy. We found that circ-ZNF609 is up-regulated in biopsies from both the two major RMS subtypes, the alveolar (ARMS) and the embryonal (ERMS), and we discovered that its knock-down blocks proliferation of an ERMS-derived cell line, while it has no effect on ARMS-derived cells. To understand the mechanism through which circ-ZNF609 affects cell proliferation we compared the different effects of circ-ZNF609 depletion in ERMS and ARMS and we identified genes and pathways on which the circRNA acts.

overall_design: Total RNA from wild-type human primary myoblasts treated either with a control siRNA (si-SCR) or with a siRNA specific for circ-ZNF609 (si-Circ) was analyzed by RNA-Seq. The experiment was performed in duplicate (4 samples in total). Total RNA from RD cells (Embryonal Rhabdomyosarcoma) and RH4 cells (Alveolar Rhabdomyosarcoma) treated either with a control siRNA (si-SCR) or with a siRNA specific for circ-ZNF609 (si-Circ) was analyzed by RNA-Seq. The experiment was repeated in duplicate (8 samples in total).

first: Ivano

last: Legnini

last: Megiorni

first: Alessio

last: Colantoni

first: Tiziana

last: Santini

first: Mariangela

last: Morlando

first: Gaia

last: Di Timoteo

first: Dario

last: Dattilo

first: Carlo

last: Dominici

first: Irene

last: Bozzoni


title: Parallel profiling of DNA methylation and hydroxymethylation highlights neuropathology-associated epigenetic variation in Alzheimer's disease.

status: Public on Mar 05 2019

city: Exeter

first: Katie

last: Lunnon

address: RILD Level 4, Barrack Road

department: Medical Research

institute: University of Exeter Medical School

summary:
Background
Alzheimer’s disease is a progressive neurodegenerative disorder that is hypothesized to involve epigenetic dysfunction. Previous studies of DNA modifications in Alzheimer’s disease have been unable to distinguish between DNA methylation and DNA hydroxymethylation. DNA hydroxymethylation has been shown to be enriched in the human brain, although its role in Alzheimer’s disease has not yet been fully explored. Here we utilize oxidative bisulfite conversion, in conjunction with the Illumina Infinium Human Methylation 450K microarray, to identify neuropathology-associated differential DNA methylation and DNA hydroxymethylation in the entorhinal cortex.
Results
We identified one experiment-wide significant differentially methylated position residing in the WNT5B gene. Next, we investigated pathology-associated regions consisting of multiple adjacent loci. We identified one significant differentially hydroxymethylated region consisting of four probes spanning 104 bases in the FBXL16 gene. We also identified two significant differentially methylated regions: one consisting of two probes in a 93 base-pair region in the ANK1 gene and the other consisting of six probes in a 99 base-pair region in the ARID5B gene. We also highlighted three regions that show alterations in unmodified cytosine: two probes in a 39 base-pair region of ALLC, two probes in a 69 base-pair region in JAG2, in addition to the same six probes in ARID5B that were differentially methylated. Finally we replicated significant ANK1 disease-associated hypermethylation and hypohydroxymethylation patterns across eight CpG sites in an extended 118 base-pair region in an independent cohort using oxidative-bisulfite pyrosequencing.
Conclusions
Our study represents the first epigenome-wide association study of both DNA methylation and hydroxymethylation in Alzheimer’s disease entorhinal cortex. We demonstrate that previous estimates of DNA hypermethylation in ANK1 in Alzheimer’s disease were underestimates as it is confounded by hypohydroxymethylation.

overall_design: This data includes 364 samples, including 176 entorhinal cortex and 188 cerebellum samples, and 20 samples where data was incomplete (e.g., did not pass QC, Braak data was missing).

first: A

middle: R

last: Smith

first: R

middle: G

first: E

last: Hannon

first: J

last: Roubroeks

last: Burrage

first: C

last: Troakes

first: S

last: Al-Sarraj

last: Mill

first: D

last: van den Hove

first: K

last: Pishva

last: Sloan


title: Global gene expression analysis in PTEN versus GFP expressing H1650 lung adenocarcinoma cells

status: Public on Oct 16 2018

city: San Francisco

first: Nilanjana

last: Chatterjee

state: CA

address: 600 16th street

department: Department of Medicine

institute: UCSF

summary: PTEN or GFP were stably expressed in PTEN-deficient lung adenocarcinoma cells by viral transfection followed by puromycin selection. Microarray analysis of total RNA isolated from H1650 cells stably expressing PTEN or GFP was performed to identify potential PTEN responsive genes.

overall_design: Three biological replicate retroviral infections of H1650 cells were performed with pBABE-PTEN or pBABE-GFP expression plasmidsollowed by selection in 2 ug/ml puromycin for 2 days. Stable PTEN expression was confirmed by immunoblot analysis 5 days post-infection.  Total RNA was isolated from each replicate using the RNeasy kit (Qiagen) according to manufacturer’s instructions. After quality control validation, total RNA was processed for labeling and hybridization on GeneChip Human Genome Arrays (HGU133 plus 2.0) followed by scanning and image quantification.

first: Trever

last: Bivona


title: RNA-seq of exosomes identifies lncRNA profiles that distinguish early-stage esophageal squamous cell carcinoma (ESCC) from non-malignant esophagitis

status: Public on Sep 27 2018

first: Rihong

last: Zhai

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the application of RNA sequencing technology for high-throughput profiling of transcriptomes in plasma exosomes from early-stage ESCC and  esophagitis.  By analyzing over 95G of clean reads (depleted rRNA), we found that expression features of exosomal lncRNAs were distinct from that of exosomal mRNAs. We identified differentially expressed exosomal lncRNAs and mRNAs for ESCC, and esophagitis. We further analyzed the biological functions of differentially expressed lncRNAs using GO, KEGG, as well as knockdown assay with siRNAs. This study provides information for identifying cancer and non-malignant disease relevant exosomal lncRNAs through integrative analyses of RNA sequencing data.

overall_design: Examination and comparison of lncRNAs and mRNAs in exosomes from ESCC, esophagitis, and healthy control, respectively.


title: Transcription profiles of rectal biopsies obtained during diagnostic colonoscopy for pediatric inflammatory bowel diseases.

status: Public on Nov 27 2018

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary: RNA was isolated from rectal biopsies from 190 pediatric patients undergoing diagnostic colonoscopy for inflammatory bowel diseases, including Crohn's disease and ulcerative colitis. Single-end, 75-bp sequencing was performed, and raw reads aligned to the human genome using Gencode v 24 as reference.  We included 14085 protein-coding mRNA genes in downstream analyses, where cutoffs of fold change>1.5 and FDR<0.05 were considered significant.

overall_design: RNA-sequencing of rectal biopsies obtained from pediatric IBD and control patients.

first: Yael

last: Haberman

first: Ted

last: Denson


title: Progressive immune activation and negative immunoregulation from common melanocytic nevi to dysplastic nevi to melanoma

status: Public on Oct 25 2018

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: The purpose of this study was to comprehensively study and compare the molecular gene expression profiles of common melanocytic nevi (GSE53223), dysplastic nevi (GSE53223), and primary melanoma.

overall_design: Whole tissue samples of 5 common melanocytic nevi and 7 dysplastic nevi (GSE53223) and 16 primary melanomas were obtained via excisional biopsy and subjected to microarray analysis.

first: Bernice

last: Yan

first: Sandra

last: Garcet


title: High throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites

status: Public on Oct 06 2018

city: Austin

first: Mia

last: Mihailovic

state: Texas

address: 200 E Dean Keeton St

department: McKetta Dept of Chem Eng

institute: UT Austin

summary: These data were obtained using a recently-developed high throughput method to probe regional RNA accessibility by mimicking in vivo antisense hybridization.  The method (INTERFACE) is an engineered RNA system (for use in E. coli) that exploits conserved bacterial mechanisms of translational stalling and Rho-dependent transcription termination mechanisms to quantify RNA hybridization (via an asRNA targeting an RNA region of interest) via a transcriptional elongation response. We first establish the high throughput system by evaluating the accessibility profile of a well-characterized gI intron (overexpressed).  We then apply this method with bioinformatics and machine learning approaches to profile over 900 RNA-interaction interfaces in 71 validated, but largely mechanistically under-characterized, sRNAs of Escherichia coli, in the presence and absence of a global regulator, Hfq. Importantly, we showcase the utility of INTERFACE in detecting RNA regions whose hybridization is Hfq-sensitive, finding two thirds of tested sRNAs with Hfq dependency. Further, we identify in vivo hybridization patterns that hallmark functional regions in 16 well-characterized sRNAs and couple these insights to a computational target prediction algorithm to identify novel mRNA targets for six under-characterized and two well-characterized sRNAs.

overall_design: Evaluation of regional accessibility profiles of a library of sRNAs in E. coli

first: Jorge

last: Vazquez-Anderson

first: Yan

last: Li

first: Victoria

last: Fry

first: Praveen

last: Vamalathas

first: Daniel

last: Herrera

first: Richard

last: Lease

first: Lydia

last: Contreras

first: Warren

middle: B

last: Powell


title: Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming

status: Public on Sep 10 2018

city: Palo Alto

first: Jifan

last: Hu

address: 3801 Miranda Ave, Bldg 100, Room E4-200

department: Palo Alto Veterans Institute for Research

institute: Stanford University Medical School

summary: RNA transcriptome sequencing (RNA-Seq) and RNA reverse transcription-associated trap sequencing (RAT-Seq) were usded to map long noncoding RNA (lncRNAs) in reprogramming of fibroblasts into pluripotency

overall_design: Fibroblasts (FIB) and induced pluripotent stem cells (iPSCs) were collected in the process of reprogramming. RNA-Seq was used to identify lncRNAs that are differentially-expressed in reprogramming. RAT-Seq was utilized to generate the database to map the regulatory element network of lncRNA candidate Osclr8 (NONMMUT043505, Platr10).

first: Zhonghua

last: Du

first: Xue

last: Wen

first: Wei

first: Jiuwei

last: Cui

first: Ji-Fan


title: Genome-wide target profiling of pluripotency-associated long noncoding RNAs by RAT-Seq

summary: Using RNA reverse transcription-associated trap sequencing (RAT-Seq), we profiled the genome-wide binding gene targets for pluripotency-associated long noncoding RNAs (lncRNAs), including Platr10 (Osclr8), Oeblr20, Oplr16, Palr35, Palr34, Peln1, and Peln4. These datasets will help study the mechanisms underlying the role of lncRNAs in the establishment and maintenance of pluripotency.

overall_design:
A RNA reverse transcription-associated trap sequencing (RAT-seq) assay [1, 2] was modified to map the genome-wide interacting gene targets for lncRNAs that are differentially expressed in reprogramming of fibroblasts into pluripotency. Cells were collected at different stages of pluripotent reprogramming, including fibroblasts and induced pluripotent stem cells (iPSCs) [3, 4]. After cross-linking with 2% formaldehyde to fix the lncRNA-chromatin structure, cells were lysed with cell lysis buffer (10 mM Tris [pH 8.0], 10 mM NaCl, 0.2% NP-40, 1x protease inhibitors). After centrifugation, nuclei were suspended in 1× reverse transcription buffer in the presence of 0.3% sodium dodecyl sulfate (SDS), and incubated at 37°C for 1 hr. Triton X-100 was then added to a final concentration of 1.8% to sequester the SDS.

The gene strand-specific reverse transcription was performed using lncRNA-specific complementary primers in the presence of biotin-dCTP. After 50 min of reverse transcription of Platr10 lncRNA with Maxima Reverse Transcriptase (Thermo Fisher Scientific, CA) at 62 C, the reaction was stopped by adding 4µl 0.5M EDTA. After nuclear lysis, the chromatin complex was subjected to sonication for 180 s (10 s on and 10 s off) on ice with a Branson sonicator with a 2-mm microtip at 40% output control and 90% duty cycle settings. The biotin-labeled cDNA/chromatin DNA complex was pulled down with biotin-streptavidin magic beads (Invitrogen, CA). After reversing the cross-links and washing with 10 mg/ml proteinase K at 65°C overnight and treatment with 0.4 µg/ml RNase A for 30 min at 37°C, the genomic DNA that interacts with the lncRNA was extracted and digested by Dpn I, and ligated with the NEBNext adaptors (NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina) to construct the library. The library DNAs were subject to Illumina sequencing (Shanghai Biotechnology, Shanghai).

As the controls, the RAT assay was performed for iPSCs and fibroblasts by replacing lncRNA-specific complimentary primers with random primers and constructed a control library for sequencing using the same protocol.

To reduce the background, the RAT-Seq data were normalized over the peaks of the control RAT-Seq data that were generated by using random oligonucleotide primers in the RAT assay. For this, differential binding analysis was performed with the DiffBind package using parameters of fold change difference ≥2 and p-value < 0.05, with false discovery rate (FDR) <0.1. The adjusted RAT-Seq data were used for mapping the lncRNA target gene interaction network.

LncRNAs and controls:
1.	Platr10 (ENSMUSG00000099370, NONMMUT043505, Osclr8, Oct4-Sox2 coating lncRNA 8): a pluripotency-associated lncRNA that is activated in pluripotent reprogramming. It binds to the regulatory elements of multiple stem cell core factor genes.
2.	Palr35 (ENSMUSG00000103968): a lncRNA that is activated in pluripotent reprogramming. However, it does not interact with the promoters of stem cell core factor genes.
3.	Oeblr20 (NONMMUG017962, Oct4 enhancer binding lncRNA 20): a pluripotent lncRNA that is activated in pluripotent reprogramming. It binds to the enhancer elements of stem cell core factor gene Oct4.
4.	Oplr16 (NONMMUT101010): a pluripotent lncRNA that is activated in pluripotent reprogramming. It binds to the promoter of stem cell core factor gene Oct4.
5.	Peln4 (NONMMUG024191): a pluripotency exit-associated lncRNA that is expressed in somatic cells, like fibroblasts. It becomes silenced in pluripotent reprogramming.
6.	Peln1 (NONMMUG035018): a pluripotency exit-associated lncRNA that is expressed in somatic cells, like fibroblasts. It becomes silenced in pluripotent reprogramming.
7.	RAT-seq random control in iPSC: A RAT-seq control library that is constructed using random oligonucleotide primers in iPSCs.
8.	RAT-seq random control in FIB: A RAT-seq control library that is constructed using random oligonucleotide primers in fibroblasts.

References:
1.	Sun J, Li W, Sun Y, Yu D, Wen X, Wang H, Cui J, Wang G, Hoffman AR, Hu JF: A novel antisense long noncoding RNA within the IGF1R gene locus is imprinted in hematopoietic malignancies. Nucleic Acids Res 2014, 42:9588-9601.
2.	Wang H, Li W, Guo R, Sun J, Cui J, Wang G, Hoffman AR, Hu JF: An intragenic long noncoding RNA interacts epigenetically with the RUNX1 promoter and enhancer chromatin DNA in hematopoietic malignancies. Int J Cancer 2014, 135:2783-2794.
3.	Zhang H, Jiao W, Sun L, Fan J, Chen M, Wang H, Xu X, Shen A, Li T, Niu B, et al: Intrachromosomal looping is required for activation of endogenous pluripotency genes during reprogramming. Cell Stem Cell 2013, 13:30-35.
4.	Du Z, Jia L, Wang Y, Wang C, Wen X, Chen J, Zhu Y, Yu D, Zhou L, Chen N, et al: Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming. Sci Data 2018, 5:180255.

first: Yanbo

last: Zhu

first: Ilkay

last: Celik

first: Jingcheng

last: Chen

first: Yichen

last: Wang

first: Lin

last: Jia

first: Cong

first: Andrew

last: Hoffman


title: Expression data of circRNA from new diagnostic AML patients (with or without EMI) and healthy volunteers

status: Public on Jul 04 2018

city: Harbin

first: Zhibo

last: Guo

state: Heilongjiang

address: No.23 Street

institute: Harbin Medical University

summary: CircRNA microarray was conducted to further explore the underlying circRNA expression alterations in extramedullary infiltration (EMI) of AML. 4 matched samples from EMI, non-EMI AML patients and healthy volunteers were selected. Mononuclear cells from 12 bone marrow samples were separated according to protocols. RNA was then extracted and hybridization for further microarray analysis.

overall_design: EMI-related circRNAs were selected by comparing with non-EMI AML patients and healthy controls. 4 independent experiments were performed using different donors for each experiment.

first: Yinghua

last: Li


title: Expression data of whole genome and circRNA from new diagnostic AML patients (with or without EMI) and healthy volunteers

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Single cell sequencing of developing heart valves identifies novel cell populations and uncovers interstitial cell heterogeneity

status: Public on Jul 13 2018

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: Our study has two main goals. The first is to define a gene expression atlas of heart valve cells and identify cell heterogeneity within postnatal heart valve development. The second is to identify interstitial cell populations involved in ECM remodeling during postnatal heart valve development.

overall_design: Using droplet RNA sequencing, transcriptomes of single cells from P7 and P30 murine aortic and mitral heart valves were analyzed.

first: Katherine

last: Yutzey

first: Alexia

last: Hulin

first: Steve

last: Potter


title: DNA N6-adenine methylation in Arabidopsis thaliana [SMRT-seq]

status: Public on Apr 16 2018

city: Singapore

first: Hao

last: Yu

address: Science Drive 4

country: Singapore

institute: National University of Singapore

type: Methylation profiling by high throughput sequencing

summary: DNA methylation on N6-adenine (6mA) has recently been found as a potentially new epigenetic mark in several unicellular and multicellular eukaryotes. However, its distribution patterns and potential functions in land plants, which are primary producers for most ecosystems, remain completely unknown. Here we report global profiling of 6mA sites at single-nucleotide resolution in the genome of Arabidopsis thaliana using single-molecule real-time sequencing. 6mA sites are widely distributed across the Arabidopsis genome and enriched over the pericentromeric heterochromatin regions. Nearly 30% of 6mA sites are present in gene bodies. Further analysis of 6mA methylome and RNA-sequencing data demonstrates that 6mA frequency positively correlates with the gene expression level in Arabidopsis. Consistently, histone variants associated with actively expressed genes interact with 6mA DNA. Our results uncover 6mA as a DNA mark associated with actively expressed genes in Arabidopsis, suggesting that 6mA serves as a novel epigenetic mark in land plants.

overall_design: SMRT sequencing in 3-week-old Arabidopsis thaliana (Col-0) wild-type

first: Zhe

last: Liang

first: Lisha

last: Shen

first: Xuean

first: Shengjie

last: Bao

first: Yuke

last: Geng

first: Guoliang

first: Fan

first: Tiegang

last: Lu

first: Xiaofeng

last: Gu


title: Association of Elevated Urinary miR-126, miR-155 and miR-29b with Diabetic Kidney Disease

status: Public on Jun 16 2018

city: Cardiff

first: Timothy

last: Bowen

address: Heath Park

institute: Cardiff University

summary: TaqMan®Array  Human  MicroRNA  Cards  were used to profile the differential expression of human microRNAs in patients with CKD versus heathy controls

overall_design: TaqMan®Array  Human  MicroRNA  Cards  Array  A  v2.1  was used to profile the expression of 377  human  microRNAs in pooled samples from 20 individual CKD patients and 20 healthy controls. This screening was used to identify new potential disease biomarkers for patients affected by CKD.  Control pool (CP)1: urine samples from 5 females of average age 44.8 years; CP2: 5 females, 57.6; CP3: 5 males, 35.2; CP4, 5 males, 53.2. Patient Pool (PP)1: urine samples from 5 CKD3 patients with an eGFR between 43.3 and 36 mL/min per 1.73m2; PP2: 5 stage 3 patients, 35 - 31; PP3: 5 stage 4/5 patients, 27.3 - 23; PP4: 5 stage 4/5 patients, 22 - 12.

first: Cristina

last: Beltrami

first: Kate

last: Simpson

first: Mark

middle: D

last: Jesky

first: Alexa

last: Wonnacott

first: Christopher

last: Carrington

first: Lucy

last: Newbury

first: Robert

last: Jenkins

first: Thomas

last: Ashdown

first: Colin

last: Dayan

first: Aled

middle: O

last: Phillips

first: Simon

last: Satchell

first: Peter

last: Corish

first: Paul

last: Cockwell

first: Donald

last: Fraser


title: Smad4 pathways modulate induction of the chemokine Ccl20 and repress inflammation-induced carcinogenesis in mouse colon

status: Public on Jun 01 2018

city: Nashville

first: Jing

last: Zhu

state: TN

institute: Vanderbilt University

summary: To understand the extent of Smad-mediated gene regulation in the colon, we isolated colon epithelium from Smad4ΔLrig1 and from Smad4+ control mice (either mice lacking a CreERT allele and treated with tamoxifen, or mice bearing a CreERT allele but treated with vehicle only) and analyzed the colonic epithelium by RNAseq. The ability of TGFβ1 and/or BMP2 to block TNF-mediated induction of Ccl20 from our study suggests that these Smad-mediated pathways may act as gatekeepers for induction of other inflammation-associated genes. To determine if Smad-mediated signaling blocks all or specific subsets of TNF-induced genes, we analyzed both colonocytes and mouse colonoid treated with or without TNF, TGFβ1, and BMP2 by RNA seq.

overall_design: In total, three RNAseq experiments were performed and three biological replicates were used for each condition: 1. Colon epithelium from Smad4ΔLrig1 and from Smad4+ control mice was isolated. Total RNA was isolated from these tissues using RNeasy kit (Qiagen). Processing of RNA using a TruSeq Stranded mRNA sample prep kit was conducted according to the manufacturer’s instructions (Illumina, San Diego, CA). 32~37 million 51 base pair single-end reads were generated per sample. 2. Total RNA was isolated from colonocytes treated with or without TNF, TGFβ1, and BMP2 using RNeasy kit (Qiagen). Processing of RNA using a TruSeq Stranded mRNA sample prep kit was conducted according to the manufacturer’s instructions (Illumina, San Diego, CA). 26~50 million 75 base pair paired-end reads were generated per sample. 3. Total RNA was isolated from mouse colonoid treated with or without TNF, TGFβ1, and BMP2 using RNeasy kit (Qiagen). Processing of RNA using a TruSeq Stranded mRNA sample prep kit was conducted according to the manufacturer’s instructions (Illumina, San Diego, CA). 50~72 million 75 base pair paired-end reads were generated per sample.

first: Anna

last: Means

first: Tanner

last: Freeman

first: Connie

last: Weaver

first: Chandrasekhar

last: Padmanabhan

first: Hanbing

last: An

first: Jinghuan

last: Zi

first: Bronson

last: Wessinger

first: Tasia

last: Brown

first: Natasha

last: Deane

first: Rupesh

last: Chaturvedi

last: Coffey

first: Keith

middle: T

last: Wilson

first: M

last: Washington

first: Chanjuan

last: Shi

first: R

last: Beauchamp


title: Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function

status: Public on May 02 2018

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3300 Hospital Dr NW

country: Canada

institute: University of Calgary - Faculty of Veterinary Medicine

summary: Ependymal cells are multi-ciliated cells that form the brain’s ventricular epithelium and a niche for neural stem cells (NSCs) in the ventricular-subventricular zone (V-SVZ). In addition, ependymal cells are suggested to be latent NSCs with a capacity to acquire neurogenic function. This remains highly controversial due to a lack of prospective in vivo labeling techniques that can effectively distinguish ependymal cells from neighboring V-SVZ NSCs. We describe a transgenic system that allows for targeted labeling of ependymal cells within the V-SVZ. Single-cell RNA-seq revealed that ependymal cells are enriched for cilia-related genes and share several stem-cell-associated genes with neural stem or progenitors. Under in vivo and in vitro neural-stem- or progenitor-stimulating environments, ependymal cells failed to demonstrate any suggestion of latent neural-stem-cell function. These findings suggest remarkable stability of ependymal cell function and provide fundamental insights into the molecular signature of the V-SVZ niche.

overall_design: We FACS collected three samples of cells from the dissociated subventricular zone of aSMACreERT2::tdTomato/Sox2-GFP mice. These included one sample of tdTomato/GFP double positive cells, and two samples of tdTomato-negative/GFP-positive cells. 10X Chromium technology was used to prepare single cell barcoded RNA sequencing libraries from each sample. These samples were subsequently sequenced on the Illumina HiSeq 2500 to a total average depth of approx. 50 million reads/sample.

first: Prajay

last: Shah

first: Jo

middle: A

last: Stratton


title: RNA-seq of Drosophila unfertilized eggs

status: Public on Jun 06 2018

first: Jun Wei

last: Pek

address: 1 Research Link National University of Singapore

institute: Temasek Life Sciences Laboratory

summary: We report the identification of stable intronic sequence RNAs (sisRNAs) in Drosophila.

overall_design: RNA was obtained from unfertilized eggs and subjected to deep sequencing.

first: Jun

middle: W


title: DNA N6-adenine methylation in Arabidopsis thaliana (methylation)

first: Hao

last: Yu

summary: DNA methylation on N6-adenine (6mA), the most prevalent DNA modification in prokaryotes, has recently been found as a potentially new epigenetic mark in several unicellular and multicellular eukaryotes. However, the distribution patterns and potential functions of 6mA in land plants, which are primary producers for most ecosystems, remain completely unknown. Here we report global profiling of 6mA sites at single-nucleotide resolution in the genomes of Arabidopsis thaliana Columbia-0 (Col), using single-molecule real-time sequencing. DNA methylome analysis shows that 6mA sites are widely distributed across the Col genomes and enriched over the pericentromeric heterochromatin regions. Nearly 30% of 6mA sites are present in gene bodies with a trend of enrichment around the transcriptional start site. In addition to a common consensus 6mA site found in other eukaryotes, novel 6mA sites were found, indicating that 6mA could evolve new functions in land plants. Further analysis of 6mA methylome and RNA-sequencing data demonstrates that 6mA positively correlates with the gene expression level in Col plants. Consistently, DNA affinity chromatography coupled with mass spectrometry reveals that histone variants associated with actively expressed genes interact with 6mA DNA. Our results uncover 6mA as a DNA mark associated with actively expressed genes in Arabidopsis, indicating that 6mA could serve as a potentially novel epigenetic mark in land plants.

overall_design: SMRT sequencing in 9-day-old Arabidopsis thaliana (Col-0) wild-type

first: Zhe

last: Liang

first: Lisha

last: Shen

first: Xuean

last: Cui

first: Shengjie

last: Bao

first: Yuke

last: Geng

first: Guoliang

first: Fan

first: Tiegang

last: Lu

first: Xiaofeng

last: Gu


title: DNA N6-adenine methylation in Arabidopsis thaliana


title: HM450K-based DNA methylation analysis of normal and Chronic Phase-Chronic Myeloid Leukemia (CP-CML)

status: Public on Mar 30 2018

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

country: France

institute: GReD CNRS

summary: We analysed genome wide DNA methylation  of mature (CD34-CD15+) and immature (CD34+CD15-) hematopoietic cells from patients with chronic phase CML at diagnosis. before any treatment. and compared it to their counterpart cells isolated from healthy donors.

overall_design: Bisulfite converted DNA  of mature (CD34-CD15+) and immature (CD34+CD15-) cells from healthy donors and CML patients was hybridized to the Infinium Human Methylation 450K BeadChip. DNA bisulfite conversion and hybridization on the arrays were performed by Integragen. SA (Evry. France) following the Illumina Infinium HD methylation protocol.

first: Franck

last: Court

first: Stéphanie

last: Maupetit-Mehouas

first: Céline

last: Bourgne

first: Marc

last: Berger

first: Philippe

last: Arnaud


title: Single-cell RNA-seq following APE1/Ref-1 knockdown in Pancreatic Ductal Adenocarcinoma

status: Public on Feb 14 2018

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

summary: APE1 was knocked down using siRNA in low passage patient-derived PDAC cells and the resulting cells, along with control cells were analysed using scRNA-seq to identify differentially expressed genes and pathways as a result of APE1 knock-down.

overall_design: siRNA APE1 knock-down versus scrambled control, The SMARTer system was used to generate cDNA from 96 captured single cells.  Unstranded 2x100bp reads were sequenced using a HiSeq2500 on rapid run mode in 1 lane.

first: Fenil

last: Shah

first: Emery

last: Goossens

middle: M

first: Michelle

last: Grimard

first: Mark

last: Kelley

first: Melissa

last: Fishel


title: Alternative NF-kB pathway hierarchy defines a DNA-binding network in Hodgkin Lymphoma

status: Public on Feb 09 2018

city: CABA

first: Stella

last: Ranuncolo

address: Potosí 4240

institute: Instituto Universitario del Hospital Italiano (IUHI)

summary: NF-kB transcription factors regulate different sets of genes in distinct germinal center derived B-cell lymphomas. ChIP-Seq and expression array data merged showed that Rel-B hierarchical network defined HL and cRel hierarchical network characterized DLBCL.

overall_design:
We sequenced the inmunoprecipitated DNA fragments by Rel-A, Rel-B, cRel, p50 and p52 antibodies in human cell lines representing Hodgkin and Non-Hodgkin Lymphoma as well as in human primary centroblasts.

Raw data files are not available for this series because they were not provided by the sequencing facility and no longer exist.

first: Weinming

last: Xiao


title: Next Generation Sequencing Facilitates Quantitative Analysis of miR-29b-1 and miR-29a targets in tamoxifen-sensitive and tamoxifen-resistant human breast cancer cells

status: Public on Aug 11 2017

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: The goal of this experiment was to identify the putative mRNA targets of miR-29b-1 and miR-29a in LCC9 tamoxifen-resistant breast cancer cell lines relative to parental MCF-7 tamoxifen-sensitive cells

overall_design: Methods: MCF-7 and LCC9 cells were transfected, in three separate experiments, with pre-miR-29b-1, pre-miR-29a, or anti-miR-29a (which blocks both miR-29b-1 and miR-29a).  RNA seq profiles were generated by deep sequencing, in triplicate, using Illumina Nextseq500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

first: Penn

last: Muluhngwi

first: Theodore

middle: S

last: Kalbfleisch

middle: C

first: Carolyn

last: Klinge


title: DNA N6-adenine methylation in 3-week-old Arabidopsis thaliana [RNA-seq]

first: Hao

last: Yu

overall_design: RNA-seq in 3-week-old Arabidopsis thaliana (Col-0) wild-type with three replicates.

first: Zhe

last: Liang

first: Lisha

last: Shen

first: Xuean

last: Cui

first: Shengjie

last: Bao

first: Yuke

last: Geng

first: Guoliang

first: Fan

first: Tiegang

last: Lu

first: Xiaofeng

last: Gu


title: ERK potentiates transactivation and oncogenic function of ERG by phosphorylation induced dissociation of PRC2 complex

status: Public on Feb 13 2018

city: Bloomington

first: Vivekananda

last: Kedage

address: 1001 E. third Street

institute: Indiana University

summary: ERK activates ERG-mediated prostate cancer specific gene expression program by phopshorylation induced dissociation of PRC2 complex

overall_design:
ChIP-Seq of transcription factor ERG and its co-repressor EZH2
RNA-seq of polyA selected RNA from RWPE1 cells expressing either empty vector, ERG-WT, ERG-S96A and ERG-S96E

first: Peter

last: Hollenhorst


title: Microarray-based gene expression on human aortic valves

status: Public on Mar 14 2018

city: Quebec

first: Yohan

last: Bossé

state: Quebec

address: 2725, chemin Sainte-Foy

institute: Laval University

summary: Aortic valves are collected from patients with severe aortic valve stenosis undergoing aortic valve replacement at the Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, Canada. From this biobank collection, transcriptomic analyses from 240 aortic valves were performed. All valves were tricuspid and had a fibro-calcific remodeling score of 3 or 4. RNA was extracted from valve leaflets and gene expression evaluated using the Illumina HumanHT-12 v4 Expression BeadChip. The main objective of this study was to perform a large-scale expression quantitative trait loci (eQTL) mapping study on human aortic valves.

overall_design: Whole-genome gene expression was performed in 240 human aortic valves.


title: DNA N6-adenine methylation in Arabidopsis thaliana (RNA)

overall_design: RNA-seq in 9-day-old Arabidopsis thaliana (Col-0) wild-type with three replicates.


title: PU.1 represses and activates gene expression in early T cells by redirection of transcription factor ensembles [ChIP-Seq]

city: Isehara

first: Hiroyuki

last: Hosokawa

state: Kanagawa

address: 143 Shimokasuya

department: Department of Immunology

country: Japan

institute: Tokai University School of Medicine

summary: Transcription factors normally regulate gene expression through their action at sites where they bind to DNA. However, the balance of activating and repressive functions that a transcription factor can mediate is not completely understood. Here, we show that PU.1 regulates gene expression in early stages of T-cell development both by recruiting partner transcription factors to its own binding sites and by depleting them from the binding sites that they may prefer when PU.1 is absent. Importantly, the loss of partner factors Satb1 and Runx1 occurs primarily from sites where PU.1 itself does not establish any detectable local binding. Genes linked to sites of partner factor ‘theft’ are enriched for considerable subsets of the genes PU.1 represses both in a model cell-line system and in normal T-cell development. Thus, system-level competitive recruitment dynamics permit PU.1 to affect gene expression both through own target sites and through action at a distance.

overall_design: anti-Runx1 ChIP-seq on Lin- bone marrow DN1 or DN3 cells.

first: Jonas

last: Ungerbäck

first: Xun

last: Wang

first: Masaki

last: Matsumoto

first: Keiichi

middle: I

last: Nakayama

first: Tomoaki

last: Tanaka

first: Ellen

middle: V

last: Rothenberg


title: Molecular changes in kidney allografts after simultaneous liver-kidney compared with solitary kidney transplantation

status: Public on Apr 14 2017

city: Rochester

first: Walter

last: Park

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

summary:
The aim of this study was to investigate correlations between early subclinical findings (10 and 90 day histology and gene expression data) and late outcomes (transplant glomerulopathy and graft loss) in positive crossmatch kidney transplants (+XMKTx).
Our goal was threefold: first, to confirm that intragraft molecular changes at 12m post-transplant are associated with the observed histologic changes in SLK transplant recipients, compared with KTA transplant recipients; second, to ascertain whether specific molecular pathways/markers that are not accounted for by routine histology are differentially expressed in the kidney allografts of the SLK transplant recipients; and third, to determine whether a molecular signature that is uniquely associated with simultaneous liver transplantation can be identified in kidney allografts.

overall_design: Biopsy samples were from positive and negative crossmatch simultaneous liver-kidney transplant recipients (12 month protocol biopsies) were compared to control patient (positiive and negative crossmatch) biopsies obtained at 12 months.

first: Timucin

last: Taner


title: Opposite functions of microglial and macrophagial TNFR2 in EAE pathogenesis: the good versus the bad.

status: Public on Nov 21 2016

city: Miami

first: Han

last: Gao

state: FL

address: 1095 NW 14th Terr

department: Miami Project to Cure Paralysis

institute: University of Miami

summary: In MS pathophysiology, soluble tumor necrosis factor (TNF) has been attributed detrimental functions, whereas transmembrane TNF promotes neurorepair primarily by activating TNF receptor 2 (TNFR2). Here we investigate the role of TNFR2 in microglia and peripheral monocyte/macrophages in EAE using novel cell-specific conditional knockouts. We show that microglial TNFR2 ablation leads to early onset of EAE, with increased CNS leucocyte infiltration, T cell activation, and demyelination. TNFR2-ablated microglia shows a more pro-inflammatory phenotype, with dysregulation of genes controlling innate immunity and host defense. Conversely, monocyte/macrophagial TNFR2 ablation results in EAE suppression, with impaired peripheral T cell activation. Our work uncovers a dichotomy of function for TNFR2 in myeloid cells, with microglial TNFR2 providing protective signals to contain disease, and monocyte/macrophagial TNFR2 driving immune activation and EAE initiation. This needs to be taken into account when targeting TNFR2 for therapeutic purposes in neuroinflammatory diseases to which both populations are key contributors.

overall_design: RNA-seq of microglia from TNFR2 KO mice and control mice at onset of EAE.

first: Matt

last: Danzi

first: Roberta

last: Brambilla


title: The meiotic recombination activator PRDM9 trimethylates both H3K4 and H3K36 at recombination hotspots in vivo

status: Public on Jun 30 2016

city: Bar Harbor

first: Natalie

last: Powers

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

summary: Mammalian genetic recombination is concentrated at hotspots, specialized 1-2 Kb sites separated by long stretches of DNA lacking recombination.  Mammalian hotspot locations depend on PRDM9, a zinc finger protein that binds at hotspots and uses its SET domain to locally trimethylate histone H3K4. Here we find that PRDM9 also locally trimethylates H3K36 at hotspots. Using ChIP-seq and immunoprecipitation data for H3K36me3 in murine spermatocytes, we show that H3K4me3 and H3K36me3 coincide only at hotspots in germ cells, and that this H3K4me3/H3K36me3-double-positive signature is almost entirely dependent on PRDM9.

overall_design:
We performed ChIP-seq with an antibody against H3K36me3, using chromatin extracted from murine spermatocytes, and compared it to previously generated ChIP-seq data for H3K4me3 in the same cell type.
----------------------------------
This dataset represents the H3K36 component only

first: Kenneth

last: Paigen


title: RNA-seq of KD, rescues of NMD factors, and UPF1-flag CLIP-seq in HeLa cells.

status: Public on Dec 19 2016

city: Bern

first: Oliver

last: Muehlemann

address: Freiestrasse 6

country: Switzerland

institute: University of Bern

summary:
This study aims at confidently identifying endogenous nonsense mediated decay (NMD) targets. To achieve this purpose, we performed KD of a few NMD factors in HeLa cells. Additionally, we performed rescue experiments for each factor, expressing an RNAi-resistant version of the gene from a plasmid.
To determine transcripts bound by UPF1 in HeLa cells, A construct with a C-terminally flag tagged version of UPF1 was expressed. In order to avoid competition with endogenous UPF1, a KD was performed.

overall_design:
KD and rescue of three NMD factors (UPF1, SMG6, SMG7), plus a combined SMG6 and SMG7 KD, with individual rescues.
2 biological replicates of UPF1-flag CLIP-seq were carried out.

first: Martino

last: Colombo

first: Evangelos

last: Karousis

last: Mühlemann


title: Klf5 regulates muscle differentiation via directly targeted muscle-specific genes in cooperation with MyoD in mice

status: Public on Oct 14 2016

city: Bunkyo

first: Yumiko

last: Oishi

state: Tokyo

address: 1-5-45, Yushima

department: Department of Cellular and Molecular Medicine

institute: Tokyo Medical and Dental University

summary: Deletion of Klf5 in satellite cells impaired muscle regeneration due to a failure of differentiation. Mechanistically, Klf5 controls transcription of muscle genes by interacting with MyoD and Mef2. These findings provide a potential intervention into the process of muscle regeneration through modulation of Klf5.

overall_design: Genome wide localization of Transcription factors Klf5 and MyoD were assessed by ChIP-Seq. Genome-wide gene expression were analyzed by RNA-seq at indicated timepoint during myoblast differentiation.


title: Diarrhoeal mechanisms of the Campylobacter jejuni enteritis

status: Public on Oct 10 2017

city: Berlin

first: Michal

middle: Ruth

last: Schweiger

address: Ihnestrasse 63-73

department: Lehrach

country: Germany

institute: Max Planck Institute For Molecular Genetics

summary: Campylobacter jejuni is the most prevalent cause of foodborne bacterial enteritis worldwide. This study aims at the characterisation of pathomechanisms and signalling in Campylobacter-induced diarrhoea in the human mucosa. During routine colonoscopy, biopsies were taken from patients suffering from campylobacteriosis. RNA-seq of colon biopsies was performed to describe Campylobacter jejuni-mediated effects. Mucosal mRNA profiles of acutely infected patients and healthy controls were generated by deep sequencing using Illumina HiSeq 2500. This data provide the basis for subsequent upstream regulator analysis.

overall_design: Colon mucosa mRNA profiles from 4 acutely infected patients and 6 healthy controls were generated by paired end sequencing using Illumina HiSeq 2500

first: Roland

last: Buecker

first: Martin

last: Kerick

first: Joerg-Dieter

last: Schulzke


title: SCL and LMO1 reprogram thymocytes into self-renewing cells.

status: Public on Nov 05 2015

city: Montreal

first: mathieu

last: tremblay

state: QC

address: 2950 Chemin de Polytechnique, pav marcelle-coutu 1432

institute: Université de Montréal/IRIC

summary: The SCL and LMO1 oncogenic transcription factors reprogram thymocytes into self-renewing pre-leukemic stem cells (pre-LSCs). Here we report that SCL directly interacts with LMO1 to activate the transcription of a self-renewal program coordinated by LYL1.

overall_design: Gene expression profiles of thymocytes from SCL-LMO1 transgenic and age-matched non transgenic Cd3ε-/- mice were compared to identify candidate genes that confer self-renewal capability to pre-leukemic thymocytes.

first: M

last: Tremblay

first: V

last: Veiga

first: S

last: Lemieux

first: T

last: Hoang


title: Gene expression data of OsGRAS23 overexpression transgenic rice plants under normal and drought stress conditions

status: Public on Dec 31 2014

city: Shanghai

first: Kai

last: Xu

address: No.2901, Beidi Rd.

institute: Shanghai Agrobiological Gene Center

summary:
GRAS transcription factors are plant-specific proteins that play diverse roles in plant development and abiotic stress responses, over-expression of OsGRAS23, a GRAS gene in rice, showed improved drought resistance.
To search the downstream genes of OsGRAS23, we performed microarray analysis of the OsGRAS23-overexpressing and wild-type plants under both normal and drought stress conditions using Affymetrix Rice Genome Genechip. 21-day-old plants of the OsGRAS23-overexpressing line OE1 as well as the wild-type plants were used in the drought treatment.

overall_design: The OsGRAS23 overexpression plants and the wild-type plants were cultured in the culture solution for 21 days. Half of the plants were sampled as the untreated control for RNA isolation, and the others were transferred onto filter papers to induce drought stress. Two biological replicate samples each from the OsGRAS23 overexpression and wild type lines were profiled using rice whole-genome microarrays.

first: Hong

middle: Y

last: Liu

first: Li

middle: J

last: Luo


title: IL-10 dysregulation in acute mountain sickness revealed by transcriptome analysis

status: Public on Mar 27 2017

city: Chongqing

first: bao

last: liu

address: 30 Gaotanyan street

department: Institute of Medicine and Hygienic Equipment for High Altitude Region

institute: 3rd Military Medical University

summary: Acute mountain sickness (AMS), which may progress to life-threatening high altitude cerebral edema, is a major threat to millions of people who live in or travel to high altitude. Although studies have revealed the risk factors and pathophysiology theories of AMS, the molecular mechanisms of it do not comprehensively illustrate. Here, we used a system-level methodology, RNA sequencing, to explore the molecular mechanisms of AMS at genome-wide level in 10 individuals. After exposure to high altitude, a total of 1,164 and 1,322 differentially expressed transcripts were identified in AMS and non-AMS groups, respectively. Among them, only 328 common transcripts presented between the two groups. Immune and inflammatory responses were overrepresented in participants with AMS, but not in non-AMS individuals. Anti-inflammatory cytokine IL10 and inflammation cytokines IF17F and CCL8 exhibited significantly different genetic connectivity in AMS compared to that of non-AMS individuals based on network analysis. IL10 was down-regulated and both IF17F and CCL8 were un-regulated in AMS individuals. Moreover, the serum concentration of IL10 significantly decreased in AMS patients after exposure to high altitude (p = 0.001) in another population (n=22). There was a large negative correlation between the changes of IL10 concentration, r(22) = -0.52, p =  0.013,  and Lake Louise Score. Taken together, our analysis provides unprecedented characterization of AMS transcriptome and identifies that genes involved in immune and inflammatory responses were disturbed in AMS individuals by high altitude exposure. The reduction of IL10 after exposure to high altitude was associated with AMS.

overall_design: Transcriptome from blood samples of AMS and non-AMS individuals were measured and analyzed before their departure and upon their arrival at high altitude (5300m).

first: Bao

first: Jian

last: Chen

first: Long

last: Zhang

first: Yixing

last: Gao

first: Jianhua

last: Cui

first: Erlong

first: Gang

first: Yan

last: Liang

first: Yu

last: Wang

first: Yuqi


title: A transcriptional signature of fatigue derived from patients with primary Sjögren's Syndrome

status: Public on Dec 31 2015

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

summary: Fatigue is a debilitating condition with a significant impact on patients’ quality of life. Fatigue is frequently reported by patients suffering from primary Sjo ̈gren’s Syndrome (pSS), a chronic autoimmune condition characterised by dryness of the eyes and the mouth. However, although fatigue is common in pSS, it does not manifest in all sufferers, providing an excellent model with which to explore the potential underpinning biological mechanisms.

overall_design:
Whole blood samples from 131 fully-phenotyped pSS patients, stratified for the presence of fatigue, collected by the UK primary Sj ̈ogren’s Syndrome Registry were used for whole genome microarray. The resulting data were analysed both on a gene by gene basis and using pre-defined groups of genes. Finally, gene set enrichment analysis (GSEA) was used as a feature selection technique for input into a support vector machine (SVM) classifier. Classification was assessed using area under curve (AUC) of receiver operator characteristic and standard error of Wilcoxon statistic, SE(W).
Contributor: The UK Primary Sjögren’s syndrome registry

first: Katherine

last: James

first: Shereen

last: Al-Ali

first: Jessica

last: Tarn

first: Colin

last: Gillespie

first: Victoria

last: Hindmarsh

first: James

last: Locke

first: Sheryl

last: Mitchell

first: Dennis

last: Lendrem

last: Bowman

first: Elizabeth

last: Price

last: Pease

first: Paul

last: Emery

first: Peter

last: Lanyon

first: John

last: Hunter

first: Monica

last: Gupta

first: Michele

last: Bombardieri

first: Nurhan

last: Sutcliffe

first: Costantino

last: Pitzalis

last: McLaren

first: Annie

last: Cooper

first: Marian

last: Regan

first: Ian

last: Giles

first: David

last: Isenberg

first: Vadivelu

last: Saravanan

last: Coady

first: Bhaskar

last: Dasgupta

first: Neil

last: McHugh

first: Steven

last: Young-Min

first: Robert

last: Moots

first: Nagui

last: Gendi

first: Mohammed

last: Akil

first: Bridget

last: Griffiths

first: Anil

last: Wipat

first: Julia

last: Newton

middle: E

last: Jones

last: Isaacs

first: Jennifer

last: Hallinan

first: Wan-Fai

last: Ng


title: Genome-wide CpG methylation during osteogenic and myogenic differentiation from adipose- derived stem cells.

status: Public on Jan 02 2014

city: L'Hospitalet de Llobregat

first: Antonio

last: Gómez

state: Barcelona

address: Av. Gran Vía s/n km. 2,7.

department: Epigenetics and Biology of Cancer Program

country: Spain

institute: IDIBELL

summary: In the current study, we have performed a high-throughput CpG methylation analysis of well characterized and defined populations of human adipose-derived stem cells (hASCs) before and after in vitro induction of osteogenic and myogenic differentiation that allows identifying DNA methylation- regulated differentiation genes. We have also address the extent of the epigenetic programming of hASCs- derived differentiated cells by comparing the methylation profiling of these cells with their somatic counterparts from primary tissues. Finally, we also compared the patterns of CpG methylation of hASCs (and their derivatives) with the methylation profiles of myosarcoma and osteosrcoma cell lines. All the CpG methylation studies have been performed with the Infinium 27K methylation arrays (from Illumina).

overall_design: DNA from adipose –derived stem cells (n=4), in vitro induced myocytes (n=3), in vitro induced osteocytes (n=3), primary osteocytes obtained from ribs (n=1), primary myocytes (n=1), osteosarcoma cell line (MG63) and myosarcoma cell lines (Te 32.T and RD) was isolated applying the QIAamp® DNA Mini Kit (Qiagen Iberia, Spain). Microarray- based DNA methylation profiling was performed with the HumanMethylation27 BeadChip Infinium Methylation Arrays® (Illumina, Inc.).The panel was designed to compare the DNA methylation status of each group of samples, which allow interrogating 27,578 CpG loci covering 14,495 genes at single-nucleotide resolution by typing bisulfite-converted DNA. The sequences included in the panel are derived from the well-annotated NCBI CCDS database (Genome Build 36) and is supplemented with more than 1,000 cancer-related genes described in published literature. Probe content has been enriched to deeply cover more than 150 well-established cancer genes known to show differential methylation patterns. Methylation array content also targets the promoter regions of 110 miRNA genes. Methylation arrays were performed as follows. Briefly, bisulfite conversion of 1 μg of genomic DNA was done using the CpGenomicTM DNA Modification Kit (Intergen Company, Purchase, NY, USA). After sodium bisulfite treatment, the remaining assay steps used Infinium technology and using Illumina-supplied reagents and conditions. A thermocycling program with a short denaturation step included for bisulfite conversion (16 cycles of 95ºC for 30 seconds followed by 50ºC for 1 hour) was performed to improve bisulfite conversion efficiency. After bisulfite conversion, each sample was whole-genome amplified (WGA) and enzymatically fragmented. The bisulfite-converted WGA-DNA samples were purified and applied to the BeadChips. During hybridization, the WGA-DNA molecules anneal to locus-specific DNA oligomers linked to individual bead types. The two bead types correspond to each CpG locus -one to the methylated and the other to the unmethylated state. Allele-specific primer annealing is followed by single-base extension using DNP- and Biotin-labeled dNTPs. Both bead types for the same CpG locus will incorporate the same type of labelled nucleotide, determined by the base preceding the interrogated cytosine in the CpG locus, and therefore will be detected in the same colour channel. After extension, the array is fluorescently stained, scanned, and the intensities of the unmethylated and methylated bead types measured. DNA methylation values, described as beta values, are recorded for each locus in each sample via BeadStudio software. DNA methylation beta values are continuous variables between 0 (completely unmethylated) and 1 (completely methylated), representing the ratio of the intensity of the methylated bead type to the combined locus intensity.

first: Manel

last: Esteller

first: María

last: Berdasco


title: Discrimination of dysplastic nevi from common melanocytic nevi by cellular and molecular criteria

status: Public on Aug 01 2014

city: New York

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: Cellular and molecular differences between DNs and CMNs are not completely understood.  Using cDNA microarray, quantitative RT-PCR, and immunohistochemistry, we molecularly characterized DNs and analyzed the difference between DNs and CMNs.

overall_design: total RNA was extratced from sliced full thickness tissue samples for both nevi samples.  total RNA was extratced from bulk puch biopsy samples for normal skin.

first: Hiroshi

last: Mitsui

last: Suárez-Fariñas

first: James

middle: G

last: Krueger


title: Single Base-Resolution Methylome of the cysticercus reveals a specific epigenomic map

status: Public on Jan 01 2017

city: shenzhen

first: Guanyu

last: Ji

state: GuangDong

address: 14th of middle jinxiu road

department: R&D

institute: GENEDOHEALTH

summary: Similar to other metazoan pathogens, cysticercus undergoes transcriptional and developmental regulation during its complex lifecycle and host interactions. DNA methylation as a mechanism to control these processes has, to date, been discounted in this parasite. Given the new availability of high-resolution methylation detection methods, here we show the first evidence for cytosine methylation in the Taenia solium genome. Transcriptional coregulation of novel DNA methyltransferase (Dnmt2), DNA Methyltransferase 3 (DNMT3) and methyl-CpG-binding domain proteins mirrors the detection of cytosine methylation abundance and implicates the presence of functional DNA methylation machinery. Here, using MethylC-seq, we present the first study to confirm the existence of DNA methylation in the cysticercus of Taenia solium genome. we conservatively estimate that 0.11% of genomic cytosines are methylcytosines, most(56%) of which occur in CpA dinucleotides.in non-expressed gene cohorts mCG hypermethlated in gene bodies. and DNA methylation level with a negtive correlation with expression, suggesting it has a positive role in gene transcription. We find that transposable elements are hypomethylated, but in contrast, ribosomal DNAs are densely methylated.  This work contributes to our understanding of epigenetics in platyhelminth such as cysticercus, which is an important human parasite. raises the possibility that targeting DNA methylation processes may be a useful strategy in therapeutics of cysticercosis.  Finally, our work constitutes the first integrated report, to our knowledge, of DNA methylation in a cysticercus, demonstrates a strategy for sequencing the epigenomes of had methylation not on CpG. provide a foundation for future studies exploring this key epigenetic modification in human cysticercus disease and development.

overall_design: Whole genome bisulfite sequencing and RNA-seq of cysticercus

first: Fei

last: Gao

first: Junwen

last: Wang


title: Biased gene expression in early honeybee larval development (sequencing)

status: Public on Nov 13 2013

city: Dunedin

first: Peter

middle: Kenneth

last: Dearden

address: 710 Cumberland St

department: Department of Biochemistry

country: New Zealand

institute: University of Otago

summary: Female larvae of the honeybee (Apis mellifera) develop into either queens or workers depending on nutrition during larval development. This nutritional stimulus triggers different developmental trajectories, resulting in adults that differ in physiology, behaviour and life-span.  To understand how these developmental trajectories are established we have undertaken a comprehensive analysis of differential gene expression throughout larval development.

overall_design: Gene expression of honeybee queen and worker larval samples was analysed at 60 hours with high-throughout sequencing

first: Rosannah

last: Cameron

first: Elizabeth

last: Duncan

middle: K


title: Characterization of a large panel of patient-derived hepatocellular carcinoma xenograft tumor models for preclinical development

status: Public on Mar 13 2014

first: Douglas

last: Fang

address: #288 FuTe Zhong Road, WaiGaoQiao Free Trade Zone

institute: WuXi AppTec Co., Ltd.

summary: We have generated a collection of patient-derived xenograft (PDX) tumor models and characterized them at the molecular level to facilitate precision oncology.

overall_design: Surgically resected HCC specimens were subcutaneously implanted in immunodeficient mice. Resulting xenografts were serially implanted to establish transplantable PDX models, which were sequentially subject to whole exome sequencing (WES), gene expression array, genome-wide human single nucleotide polymorphism (SNP) array 6.0, and serum a–fetoprotein (AFP) detection assay. The feasibility as a preclinical model was validated by efficacy studies using a standard-of-care (SOC) and a targeted agent, respectively.

middle: D

first: Bin

last: Zhang

first: Qingyang

last: Gu

first: Qiang

last: Xu

first: Yexiong

last: Tan

first: Hongye

last: Sun

first: Qin

last: Luo

first: Jian

last: Li

first: Lei

last: Chen

first: Xiaowei

first: Guibai

last: Liang

first: Shu-Hui

first: Hongyang

first: Chi-Chung

last: Chan


title: Biased gene expression in early honeybee larval development (microarray)

first: Peter

overall_design: Gene expression of honeybee queen and worker larval samples was analysed at seven time points during larval development (6 hr, 12 hr, 36 hr, 60 hr, 84 hr, 108 hr and 132 hr)


title: BY4741 and BY4741（Δyrr1）transcriptional differences under vanillin stress

status: Public on Jun 12 2017

city: Jinan

first: Xiaoming

last: Bao

state: Shandong

address: Shanda Nan Road 27

department: State Key Laboratory of Microbial Technology

institute: Shandong University

summary: BY4741（Δyrr1）exhibited better vanillin tolerance to vanillin than that of wildtype strain. To assess transcriptional differences between these two strains. Yrr1p is a transcriptional factors which activated genes related to multidrug resistance.The transcriptome of BY4741 and BY4741（Δyrr1）under vanillin stress or vanillin free conditions were conducted,respectively

overall_design: BY4741 was the control strain and BY4741（Δyrr1） was the experimental strain. The transcriptome resequencing of every strain was conducted in two conditions: under 5mM vanillin stress or vanillin free. The comparisons were: BY4741 vs. BY4741（Δyrr1）under vanillin stress or vanillin free condition; vanillin stress vs. vanillin free condition in BY4741 or BY4741（Δyrr1,respectively.The samples were collected when OD600 reach 1.6-2.0.Each strain under each condition had duplicates.The medium was SD.

first: Xinning


title: Intragraft Gene Expression in Positive Crossmatch Kidney Allografts:  Ongoing Inflammation Mediates Chronic Antibody-Mediated Injury

status: Public on May 30 2012

first: Walter

last: Park

summary: We studied intragraft gene expression profiles of positive crossmatch (+XM) kidney transplant recipients who develop transplant glomerulopathy (TG) and those who do not.  Whole genome microarray analysis and quantitative rt-PCR for 30 transcripts were performed on RNA from protocol renal allograft biopsies in 3 groups: 1) +XM/TG+ biopsies before and after TG; 2) +XM/NoTG; and 3) negative crossmatch kidney transplants (control).  Microarray comparisons showed few differentially expressed genes between paired biopsies from +XM/TG+ recipients before and after the diagnosis of TG.  Comparing +XM/TG+ and control groups, significantly altered expression was seen for 2,447 genes (18%) and 3,200 genes (24%) at early and late time points, respectively.  Canonical pathway analyses of differentially expressed genes showed inflammatory genes associated with innate and adaptive immune responses.  Comparing +XM/TG+ and +XM/NoTG groups, 3,718 probe sets were differentially expressed but these were over-represented in only 4 pathways.  A classic accommodation phenotype was not identified.  Using rt-PCR, the expression of inflammatory genes was significantly increased in +XM/TG+ recipients compared to control biopsies and to +XM/NoTG biopsies.  In conclusion, pre-transplant DSA results in a gene expression profile characterized by inflammation and cellular infiltration and the majority of XM+ grafts are exposed to chronic injury.

overall_design: We analyzed gene expression from 2 groups of positive crossmatch kidney transplant recipients (+XM/TG+ and +XM/TG-).  Patients in the +XM/TG+ group had 2 biopsies - prior to the development of transplant glomerulopathy on biopsy (Biopsy 1; cg=0; n=10) and after development of transplant glomerulopathy (Biopsy 2; cg>0; n=10).  The +XM/TG- patients had only a Biopsy 2 (cg=0; n=11).  A third patient group served as controls (n=10) and were from -XM recipients.

first: Patrick

last: Dean

first: Lynn

last: Cornell

first: James

last: Gloor

first: Mark

last: Stegall


title: Early Subclinical Inflammation Correlates with Outcomes in Positive Crossmatch Kidney Allografts

status: Public on Jun 08 2016

summary: The aim of this study was to investigate correlations between early subclinical findings (10 and 90 day histology and gene expression data) and late outcomes (transplant glomerulopathy and graft loss) in positive crossmatch kidney transplants (+XMKTx).

overall_design:
Samples from positive crossmatch kidney transplant biopsies (10d or 90d protocol biopsies) were compared to control (negative crossmatch) biopsies obtained at 90d.

The experimental design includes patients on or off a C5 inhibitor (Eculizumab). At 10d the XM+ patients are NoC5 or C5+_ON. At 90d the XM+ patients are NoC5 or C5+_On (still on the drug at 90d) or C5+_Off (originally treated with C5 but now off drug).


title: Mild food restriction and gene expression profile (liver)

status: Public on Sep 30 2009

city: bunkyo-ku

first: Kenji

last: Saito

department: Department of Applied Biological Chemistry

institute: The Univeristy of Tokyo

summary: The aim of this study is to obtain the gene expression profiles of the liver of young growing rats after mild restriction of food intake for one week or one month.

overall_design: Male Wistar rats, at 6 weeks of age, were fed with reduced diet (5%, 10%, 20% and 30% restriction) for one week or one month (n=5). After 16h fasting, the liver was then extracted and total RNA was isolated using an RNeasy mini kit with DNase treatment (QIAGEN). The RNA samples were pooled from five rats for each group. Then, DNA microarray analysis was performed using duplicate GeneChips (Affymetrix) on each pooled RNA sample.

first: Yutaka

last: Ohta

first: Manabu

last: Sami

first: Tomomasa

last: Kanda

first: Hisanori

last: Kato


title: Expression of proinflammatory genes in epidermal keratinocytes is regulated by the hydration status.

status: Public on Dec 01 2012

city: Chicago

first: Wei

last: Xu

state: IL

address: 303 E Chicago Ave, Tarry 4-714

department: Surgery

institute: Northwestern University, Feinberg School of Medicine

summary:
We hypothesized that treatment of the injured skin with occlusion limits TEWL and results in a phenotype of epithelial response that more closely resembles mucosa. Here we addressed whether different hydration conditions change gene expression patterns in epidermis using microarray study in rabbit partial-thickness incisional wound. Microarray on epidermis showed that global expression patterns of the genes in full occluded vs. non-occluded wounds are distinct. Many genes - including IL-1β, IL-8, TNF-α, and COX-2-upregulated in skin environment were also upregulated in non-occluded wounds. Simulating increased TEWL showed increased expression of proinflammatory genes in human ex vivo skin culture (HESC) and stratified keratinocytes.
Microarray on epidermis showed that global expression patterns of the genes in full occluded vs. non-occluded wounds are distinct.

overall_design:
Female New Zealand White rabbits (3-4 kg) were purchased from Covance (Princeton, NJ) and were acclimated for a minimum of 7 days prior to experiments. Ketamine (45 mg/kg) and xylazine (7 mg/kg) were injected intramuscularly as primary anesthesia method prior to the procedure. The procedure was performed while the animal was in full anesthesia with the vital sign checking every 15 min including heart beat, breath frequency, and body temperature. Buprenex (0.05 mg/kg) was applied by intradermal injection prior to the surgery and continued every 6-12 hours for 24 hours after surgery. The animals were all monitored closely for signs of discomfort post surgeries. Tissue harvests were performed following euthanasia.
The superficial incisional grids on rabbit ear were created by using a double blade scalpel with 1 mm space between the two blades. A single layer of Tegaderm was used to cover the wounding areas on both right and left ears until the wounding areas were fully re-epithelialized (two days post wounding, POE0). Thereafter, the Tegaderm on right ear was completely removed (NOW) while four more layers of Tegaderms were applied on left ear wounds (FOW). Rabbit ear samples were harvested at POE0, POE3 and POE5.

first: Shengxian

last: Jia

first: Ping

last: Xie

first: Aimei

last: Zhong

first: Robert

last: Galiano

first: Thomas

middle: A

last: Mustoe

first: Seok

last: Hong


title: Genomic Transcriptional Profiling Identifies a Blood Biomarker Signature for the Diagnosis of Septicemic Melioidosis

status: Public on Jul 01 2009

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary: Melioidosis is a severe infectious disease caused by Burkholderia pseudomallei, a gram-negative bacillus classified by the NIAID as a category B priority agent. Septicemia is the most common presentation of the disease with 40% mortality rate even with appropriate treatments. Faster diagnostic procedures are required to improve therapeutic response and survival rates. We have used microarray technology to generate genome-wide transcriptional profiles (>48,000 transcripts) of whole blood obtained from patients with septicemic melioidosis (n=32), patients with sepsis caused by other pathogens (n=31), and uninfected controls (n=29). Unsupervised analyses demonstrated the existence of a whole blood transcriptional signature distinguishing patients with sepsis from control subjects. The majority of changes observed were common to both septicemic melioidosis and sepsis caused by other infections, including genes related to inflammation, interferon-related genes, neutrophils, cytotoxic cells, and T cells. Finally, class prediction analysis identified a 37 transcript candidate diagnostic signature that distinguished melioidosis from sepsis caused by other organisms with 100% and 78% accuracy in training and independent test sets, respectively. This finding was confirmed by the independent validation set, which showed 80% prediction accuracy. This signature was highly enriched in genes coding for products involved in the MHC Class II antigen processing and presentation pathway. Transcriptional patterns of whole blood RNA distinguish patients with septicemic melioidosis from patients with sepsis caused by other pathogens. Once confirmed in a large scale trial this diagnostic signature might constitute the basis of a differential diagnostic assay.

overall_design: Whole blood obtained from patients with sepsis caused by B.pseudomallei or other pathogens were collected. mRNA Expression level of each patient was determined and compared to mRNA expression level from uninfected control including patient who had recovered from melioidosis, patient diagnosed type 2 diabetes, and healthy donors suing microarray analysis.


title: Fibrosis with Inflammation at One Year Predicts Transplant Functional Decline

status: Public on Nov 01 2010

city: Rochester

first: Walter

last: Park

address: 200 1st ST SW

institute: Mayo Clinic

summary: We previously observed reduced graft survival for kidney transplants having interstitial fibrosis with subclinical inflammation, but not fibrosis alone, on 1-year protocol biopsy. The current study aimed to determine whether fibrosis with inflammation at 1 year is associated with renal functional decline in a low-risk transplant cohort and to characterize the nature of the inflammation. Subjects were living-donor, tacrolimus/mycophenolate-treated transplant recipients without overt risk factors for reduced graft survival (n=151). Transplants with normal histology (n=86) or fibrosis alone (n=45) on 1-year protocol biopsy had stable renal function between 1 and 5 years, while those having fibrosis with inflammation (n=20) had declining glomerular filtration rate and reduced graft survival. Immunohistochemistry confirmed increased interstitial T-cells and macrophages/dendritic cells in the fibrosis with inflammation group. Gene expression was performed on a subset of biopsies in each group and demonstrated increased expression of transcripts related to innate and cognate immunity in transplants having fibrosis with inflammation. Pathway- and pathological process-specific analyses of microarray profiles revealed that, in fibrosis with inflammation, over-expressed transcripts were enriched for potentially damaging immunological activities including Toll-like receptor signaling, antigen presentation/dendritic cell maturation, interferon gamma-inducible response, cytotoxic T lymphocyte-associated and acute rejection-associated genes. Thus, fibrosis with inflammation in 1-year protocol biopsies is associated with reduced graft survival and function and with a rejection-like gene expression signature even in recipients with no clinical risk for inferior outcome. Early interventions aimed at altering rejection-like inflammation may favor improved long-term KTx survival.

overall_design: We analyzed gene expression from a group of 65 renal transplant recipients. Patient groups were carefully selected to include patients on the same immunosuppression (Prograf-MMF-Pred), transplant type (LD), absence of over post-transplant complications (AR, BK, DGF).  For each patient a 1 year protocol biopsy was examined by conventional histology and gene expression.  By histology the patients were categorized as histologically normal (n=25, i/cg/ci=0), IF/TA (n=24, i/cg=0, ci>0) and IFTA+i (n=16, cg=0, i/ci>0).

first: Matthew

last: Griffin

first: Fernando

last: Cosio


title: Molecular Criteria for Defining the Naive Human Pluripotent State [methylation profiling]

status: Public on Aug 16 2016

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Naive human pluripotent cells have been isolated in culture, but it remains unclear to what extent they resemble pluripotent cells in vivo. Here we present three lines of evidence indicating that naive pluripotent stem cells generated by small molecules share defining molecular signatures with the human preimplantation embryo. First, a comprehensive analysis of the transposcriptome reveals that naive human cells display a unique transposon expression profile of cleavage stage embryos. Second, induction of naive pluripotency is accompanied by a genome-wide depletion in DNA methylation that is reversible upon differentiation except at imprinted regions. Third, allele-specific analysis demonstrates that female naive cells exhibit an X chromosome signature of the human preimplantation embryo. However, when introduced into mouse embryos the naive cells failed to efficiently generate interspecies chimeras. Our work provides a set of molecular benchmarks for evaluating the developmental identity of distinct human pluripotent states captured in vitro.

overall_design: Examine the methylomes of 6 naïve, 2 primed and 2 re-primed human embryonic stem cells

first: Thorold

middle: W

last: Theunissen

first: Marc

last: Friedli

first: Yupeng

last: He

first: Evarist

last: Planet

first: Ryan

last: Oneil

first: Styliani

last: Markoulaki

first: Haoyi

last: Wang

first: Julien

last: Pontis

first: Alexandra

last: Iouranova

first: Michaël

last: Imbeault

last: Duc

first: Malkiel

last: Cohen

first: Katherine

last: Wert

first: Rosa

last: Castanon

first: Zhuzhu

last: Zhang

first: Dorothea

last: Maetzel

first: Yanmei

last: Huang

last: Nery

first: Jesse

last: Drotar

first: Tenzin

last: Lungjangwa

first: Didier

last: Trono

first: Rudolf

last: Jaenisch


title: Biased gene expression in early honeybee larval development

first: Peter

last: Dearden

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series